Transfer all your saves and games using QCMA to your PC. Henkaku can't be "saved" as it doesn't save to the memory card, but all you have to do is just reinstall it via the web browser when you switch to the new memory card so it's no big deal or anything.

That's a bummer. I thought making a backup via qcma is like creating an image of the card, since the resulting file is encrypted on my pc.

If it only copies official files, I'm assuming changes I've made to the other partitions wouldn't be copied either? I wish there's an easier way to go about this since I can't really compare the contents side by side...